Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-26

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Time Nick Message
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08:26 jonalv egonw, ping
08:26 egonw pong
08:26 jonalv about this CDK Extension plugins
08:26 jonalv why can't we use svn:externals?
08:26 egonw one could
08:27 jonalv but?
08:27 egonw it makes git more difficult, but no principle reasons not to use it...
08:28 jonalv I thought it would make things easier but I don't really know
08:28 * olas doesn't care
08:29 jonalv egonw, where in cdk is this boundle located?
08:29 olas egonw: did you not write about this on the wiki?
08:29 olas if not, please do
08:29 olas and email bioclipse-devel
08:29 egonw yes
08:30 egonw in the wiki I added details on org.openscience.cdk
08:30 jonalv so it's directly under trunk?
08:30 * jonalv is looking at the wiki
08:30 jonalv but he isn't sure it's complete
08:31 olas check out trunk, it will be picked up as org.openscience.cdk
08:31 jonalv cdk is a osgi boundle? cool!
08:33 olas there's a .project so it's an eclipse project
08:33 olas there's also a plugin. xml
08:34 olas and a manifest
08:34 olas so yes, it's a bundle
08:34 egonw yeah, the full monty
08:34 * jonalv mumbles something about how slow sourceforge is
08:34 olas however, it does not compile here
08:34 egonw oh, crap
08:34 * egonw will add another note
08:34 egonw run the ant task 'javacc'
08:38 egonw http://wiki.bioclipse.net/index.php?title=Checking​_out_Bioclipse_2#Getting_the_CDK_Extension_Plugins
08:42 olas egonw: nope, still compile errors
08:42 egonw can you list one or two of them?
08:45 thomas_ku joined #bioclipse
08:50 olas egonw: seems no jars are imported
08:50 olas hmm
08:50 olas let me check
08:51 egonw mmm... there should be a proper .classpath in SVN
08:51 olas ok
08:51 olas the moby project have different .project for Eclipse-building and building with ant outside eclipse
08:51 olas but I have no idea why
08:52 olas ok, here thay come
08:52 olas import com.sun.tools.doclets.Taglet;
08:52 olas not resolved
08:52 egonw ah...
08:52 egonw please verify you have this line in your .classpath:
08:52 olas import org.xmlpull.v1.XmlPullParser;
08:52 olas not resolved
08:52 egonw <classpathentry kind="lib" path="develjar/com-sun-javadoc.jar"/>
08:52 egonw <classpathentry kind="lib" path="develjar/com-sun-tools-doclets-Taglet.jar"/>
08:53 olas are they listed in the manifest?
08:53 olas all must be listed there
08:53 egonw ack
08:53 egonw hang on
08:53 olas eclipse builds the classpath from the manifest.mf
08:54 olas PDE -> update classpath does this operation
08:54 egonw ack
08:54 olas but it's posible to add stuuf to the CP anyway
08:54 egonw adding the missing jars
08:54 olas ack
08:55 egonw olas: please update CDK to 11166
08:56 olas latest?
08:56 egonw yes
08:56 olas ok
08:58 olas egonw: if you do update CP, does it compile then for you?
08:58 egonw mom
09:08 olas egonw: let me know if update CP works for you, here it doesn't
09:08 egonw yes, seems to work here
09:09 olas ok, will post my errors
09:09 olas mom
09:10 olas import org.openscience.cdk.smiles.​smarts.parser.SMARTSParser;
09:10 olas strange
09:10 olas that class seems to be missing
09:10 olas or not generated?
09:11 olas I have the jj and jjt files
09:12 olas seems liek some probs with the IUPAC parser as well
09:12 olas which has jj
09:12 olas what is that btw?
09:13 olas JJTree?
09:13 egonw source for the compiler compiler
09:14 olas any idea bout the error?
09:14 egonw seems running of the javacc task did not work...
09:14 olas will try again
09:15 egonw oh... did you hit F5 ?
09:15 egonw to refresh the Navigators list of files?
09:15 olas no
09:15 olas just found out
09:15 olas ok, now it works
09:15 egonw adding that to the wiki
09:15 olas good
09:16 egonw done
09:16 olas egonw: do you have this for cdk10 as well?
09:16 olas or are we using svn:externals there?
09:17 egonw the latter
09:17 olas egonw: did you update references to cdk in other plugins?
09:17 egonw yes
09:17 olas ok
09:17 * olas is updating
09:17 egonw might have missed one or two...
09:18 egonw but at least structdb, sdf and jchempaint should be fine
09:18 olas jmol?
09:19 egonw too, IIRC
09:19 olas ok
09:27 olas brb
09:27 olas left #bioclipse
09:29 jonalv so I should remove net.bioclipse.cdk from my workspace now?
09:30 egonw yes
09:30 egonw thanx for the reminded
09:30 egonw need to remove it from SVN
09:31 jonalv is net.bioclipse.cdk.business updated?
09:32 egonw yes, should be
09:32 jonalv oki good
09:33 CIA-46 bioclipse: egonw * r5696 /bioclipse2/trunk/plugins/net.bioclipse.cdk/:
09:33 CIA-46 bioclipse: Removed; use https://cdk.svn.sourceforge​.net/svnroot/cdk/cdk/trunk instead. See
09:33 CIA-46 bioclipse: http://wiki.bioclipse.net/index.php?title=Checking​_out_Bioclipse_2#Getting_the_CDK_Extension_Plugins
09:34 jonalv egonw, about the jchempaint in the single entry tab in the sdf editor. How do I do any editing?
09:35 egonw IIUOC, click an entry and go to the second tab
09:35 egonw IIUOC := if I understood Ola correctly :)
09:35 jonalv hm no I don't even get the single entry just grey
09:35 egonw ah... nice
09:35 egonw then you have the same problem I ran into
09:35 jonalv "IIUOC"?
09:36 jonalv ah okey :)
09:36 egonw have been looking into that... but no idea what goes wrong...
09:36 egonw events seem to be passed around correct...
09:36 egonw and I don't get any stack traces...
09:36 egonw not even when in debug mode :(
09:36 jonalv but how do I edit once I have a single entry?
09:36 jonalv I can't click anything...
09:37 egonw the Ola has not routed the mouse events yet, I think...
09:38 jonalv can he do that? Wasn't there something about OSX?
09:38 egonw yeah, may be...
09:38 egonw I guess he can't...
09:39 jonalv troublesome...
09:46 * jonalv -> lunch
10:16 olas joined #bioclipse
10:31 CIA-46 bioclipse: ospjuth * r5697 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (2 files in 2 dirs):
10:31 CIA-46 bioclipse: Added action, toolbar item, and context menu for open and export actions. Export
10:31 CIA-46 bioclipse: action should allow to extract one or more entries from SDFile to another file,
10:31 CIA-46 bioclipse: but not implemented yet. Page switch also fails to update editor tab. Very
10:31 CIA-46 bioclipse: strange.
11:35 CIA-46 bioclipse: ospjuth * r5698 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (2 files in 2 dirs): Constructed a FileDialog to save files with workspace as root folder.
11:43 * jonalv -> back
12:31 olas egonw: jonalv cannot edit in JCP at all!!!
12:31 olas very bad
13:02 egonw mmm...
13:37 olas egonw: could you assist wth that?
13:37 egonw yes, will look into that this week.
13:38 egonw please realize that this JCP code is as new and ugly to me, as it is to you...
13:38 egonw there simply are too many layers...
13:38 egonw the API is not right...
13:38 egonw which I try to solve with JCP3
13:39 egonw but that will take some more time, as I have to do that in evening hours... actually, getting JCP2 in BC2 going too...
13:39 egonw any help here is most welcome...
13:39 olas egonw: next week on monday morning is some sort of deadline for me
13:39 olas what is the problem?
13:39 egonw wish I knew
13:39 egonw the visible parts of the problems:
13:39 olas can you not edit at all?
13:40 egonw grey screen when going to the second tab in the SDF editor
13:40 * olas is on mac so please explain what you do
13:40 egonw and that jonalv cannot edit in the MDLEditor
13:40 olas does JCP for mol-files work?
13:40 egonw have not verified the latter on my machine...
13:40 olas single molfiles?
13:40 egonw but MDLEditor worked for me
13:40 olas please verify this
13:40 egonw jonalv: please explain step-by-step what you did
13:40 olas jonalv: yes, please do
13:41 olas jonalv: PING
13:44 jonalv olas: pong
13:45 * jonalv is gonan update everyting and retry
13:57 olas excellent
13:57 * olas is adding an extract action
13:58 CIA-46 bioclipse: ospjuth * r5699 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Catch NPE if setDirty on non-initialized JCPModel.
14:00 CIA-46 bioclipse: ospjuth * r5700 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.sdfeditor/src/net/bioclipse/cdk10/sdfeditor/ (4 files in 2 dirs): Added extractAction that allows for exporting of selected entries in StructureTable and save as individual molfiles.
14:05 olas jonalv: how's progress?
14:05 olas can you verify?
14:07 jonalv I am having problems getting cdk10.sdfeditor compiling
14:07 jonalv It jsut finnished building now
14:08 jonalv so hang on, it's really slow
14:08 jonalv I probably should close the runn Eclipse isntance...
14:08 * jonalv is closing Brunn Eclipse instance...
14:12 egonw mdleditor is working for me
14:12 egonw except that the dirty flag is not set...
14:12 * egonw has to leave now
14:12 egonw and pick up kids from school
14:13 jonalv The import net.bioclipse.ui.dialogs.WSFileDialog cannot be resolved
14:13 egonw not sure why the dirty flag is no longer set...
14:14 egonw bbl
14:15 jonalv so net.bioclipse.structurdb is off course not working any longer because there is not net.bioclipse.cdk
14:16 jonalv but what is more strange is that I can't get net.bioclipse.cdk10.sdfedito​r.editor.StructureTablePage to compile due to: The import net.bioclipse.ui.dialogs.WSFileDialog cannot be resolved
14:17 jonalv olas: ping?
14:19 olas pong
14:19 jonalv you know anything about why I can't get things to compile?
14:20 olas mom
14:20 * jonalv is updating again...
14:20 * olas is committing
14:20 CIA-46 bioclipse: ospjuth * r5701 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (2 files in 2 dirs): Added WSFileDialog.
14:23 olas works?
14:24 jonalv Building Workspace...
14:24 jonalv yup
14:24 jonalv gonna try to run it now then :)
14:26 jonalv I still could not edit anything. And no I got the grey screen
14:26 jonalv How am I supposed to edit?
14:26 jonalv Maybe I jsut don't understand
14:28 jonalv also, I can not traverse the file in the Single Entry tab
14:31 olas jonalv: have you tried a SINGLE molecule in MDL format, NOT an SDF?
14:31 jonalv nope
14:31 olas please do it then
14:31 olas *sigh* this is the forth time I'm asking this
14:32 jonalv is it?
14:32 olas at least
14:32 jonalv wow cool I can edit and stuff
14:32 olas SDF != MDL
14:32 olas oh, good
14:32 olas *SIGH*
14:32 jonalv I thought it was sdf we where doing...
14:32 olas that means it's just the SDFileEditor that's messed up
14:33 olas jonalv: we are not just doing one thing
14:33 olas please
14:34 olas but good, JCP works at least
14:34 jonalv olas: Okey I didn't understand that. I am sorry it's not easy for a bear with a very small brain
14:34 olas now, here comes the problem: editing in JCP dows not work in SFileEditor
14:34 olas and it is the switch of JCPModel that messes things up
14:34 olas with listeners, models, redraw
14:34 jonalv Was I supposed to get the toolbar as well?
14:35 olas not in SDFileEditor
14:35 jonalv don't I need it?
14:35 olas ??
14:35 jonalv don't we need the toolbar in order to edit?
14:35 olas no
14:35 olas you can click anyway
14:35 olas I guess
14:35 olas or maybe not
14:36 jonalv okey... so what's the toolbar for in the first place then?
14:36 * olas is frustrated that JCP is not working on Mac
14:36 jonalv you should run parallels
14:36 olas egonw: do we need spend all this time on JCP?
14:36 olas when will JCP4SWT be ready?
14:37 olas how much works of JCP3 and how much needs be done?
14:38 olas egonw?
14:38 jonalv he is picking up his children
14:39 jonalv brb
14:42 olas oh
14:42 egonw back for a short while...
14:44 egonw olas: this SDF editor things is why I suggested to have SDF import into DB, and then open one entry in a MDLEditor...
14:45 egonw the JCP3 editor stuff will take 3 months... for a FTE
14:46 egonw lot's of editing stuff to port...
14:46 egonw BC2 can't wait on that...
14:46 egonw so, we'll have to do with JCP2
14:49 olas egonw: we are close to getting this to work
14:49 olas only problem is:
14:49 olas we need a way to remove current JCPModel and its listeners, and replace with a new JCPModel with ne listeners
14:49 olas I think I'm very close
14:49 olas but there is obviously a bug left
14:50 olas but I can't solve it as I'm on Mac, and hence can't edit
14:50 olas so I need help
14:50 olas it works in JCP
14:50 olas so, it can work in StructureTable page #2
14:50 olas do you not agre?
14:52 egonw there is a helper method for that...
14:52 egonw mom
14:53 egonw cdk10.jchempaint.ui.editor.JCPP​age.updateJCPModel(IChemModel)
14:53 egonw but I believe the SDFEditor was laready using that...
15:03 jonalv olas: Wouldn't it help you very much to use parallels or something like that and thus be able to edit? Is that very hard?
15:12 egonw what are parallels?
15:12 jonalv running windows and linux inside OS X
15:12 egonw ah, right
15:12 jonalv or paralel to OS X I guess :)
15:12 egonw he was waiting for an OS upgrade, I think
15:13 olas yes
15:13 olas I've told jonalv many times
15:13 olas never take the time to upgrade OS
15:13 olas will be a day off
15:13 * jonalv still thinks that might be the easisest solution...
15:13 olas and no time for that currently
15:13 olas after next week
15:13 egonw olas: schedule a day for it...
15:13 egonw so, that nothing can come in between
15:14 * olas is messing with the JCPMultiPageEditorContributor
15:14 olas I think this is the problem
15:14 jonalv olas: install it on one of the other mac lying around...
15:14 olas which one?
15:14 jonalv the one Arvid isn't using
15:16 * olas just made Eclipse crash on tab switch in StructureEditor
15:16 jonalv Eclipse?
15:16 jonalv wow
15:16 egonw cool
15:16 * egonw is impressed
15:19 olas hmm, bioclipse
15:20 jonalv ah
15:20 olas but that is Eclipse-based so could easily get eclipse to crash as well
15:20 olas if I wanted
15:20 * olas doesn't want that
15:22 egonw right
15:22 * egonw suspects a SWT/AWT bridge bug in the Eclipse for Mac
15:22 egonw as there have been *many* for the other platforms too...
15:23 * olas fixed the nasty bug
15:24 egonw you have?
15:24 * egonw is really interested in knowing the cause...
15:25 * egonw is away... will be back later tonite
15:25 egonw will see the patch
15:44 olas jonalv; around?
15:44 jonalv olas: yup I just got 96-well result import working in Brunn :)
15:53 olas cool
15:56 CIA-46 bioclipse: ospjuth * r5702 /bioclipse2/trunk/plugins/ (26 files in 6 dirs): Large experimental commit to get editing working in SDFEditor JCPPage. Now uses JCPMultiPageActionContributor.
15:57 olas jonalv: please test this
15:57 jonalv I am on it
16:01 jonalv the normal jchempaint doesn't seem to become dirty but that is known I guess?
16:03 jonalv yes I can edit and it saves something but it didn't feel right
16:04 jonalv It is definitly a big step in the right direction!
16:04 jonalv olas++
16:05 olas :-)
16:05 olas hmm
16:05 olas jcp doesn't get dirty?
16:05 olas what do you mean?
16:05 olas for MDL?
16:05 jonalv It doesn't get an *
16:05 olas in MDL?
16:05 olas or SDF?
16:05 jonalv both
16:05 jonalv ot netiher :)
16:05 olas that should work in at least MDL...
16:06 olas did it work before?
16:06 jonalv hang on I will check again then
16:06 olas please revert commit and test
16:07 jonalv okey revert to what?
16:07 * jonalv hasn't followd up here copletely...
16:07 olas lats commit
16:07 olas r5702
16:08 olas so revert to 5701 :-)
16:08 olas just to know if my last commit broke anything in JCP
16:08 * jonalv is learning how to do that from the prompt
16:08 olas it used to work in MDL I'm quite certain
16:09 * jonalv is updteing to 5701 :)
16:10 * jonalv is building 5701 :)
16:12 jonalv it doesn't get dirty in this version either
16:12 olas hmm
16:12 olas ok
16:12 olas that used to work acording to egon
16:12 jonalv okey
16:12 olas Maybe I've broken something earlier...
16:12 olas hmm
16:12 olas can you test to revert to...
16:13 olas date yesterday?
16:13 olas all cdk-based
16:13 olas and see if edior gets dirty there
16:13 jonalv I change complete bioclipse checkout at the same time :)
16:16 jonalv Iäll go back to how things locked friday and check
16:23 jonalv it didn't work in the version from friday either
16:23 jonalv so I don't think you broke something now
16:24 olas thx
16:25 olas what was wrong when saved in SDFeditor?
16:25 olas properties are lost, I know that
16:25 olas but the structures?
16:25 jonalv itm ight just have been the layout of the atoms
16:25 jonalv I am not sure
16:25 olas could you edit the first structure, save, close, open ,look?
16:25 jonalv yea I am gonan try that a bit
16:25 olas thx
16:26 olas this really helps me
16:28 jonalv but I can't switch between the two tabs, I get a grey screan second time I enter Single entry tab
16:28 jonalv I don't think there was anything wrong with the save functionality
16:29 jonalv I think I either did wrong or found a quirk in JChemPaint
16:29 olas ok
16:29 olas talk more tomorrow
16:29 olas gotta sign out now
16:29 jonalv how big sdf-files have you tested?
16:29 olas 5 mols only
16:30 olas :-)
16:30 jonalv I am trying a big one
16:30 jonalv and nothing happens
16:30 olas oh
16:30 olas ok
16:30 olas will look at that 2morrow
16:30 olas bye!
16:30 olas left #bioclipse
18:17 rojasm joined #bioclipse

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